Variant report

Variant	rs28668949
Chromosome Location	chr5:119590208-119590209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10041241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10042714	1.00[EUR][1000 genomes]
rs10053092	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10054975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055228	1.00[EUR][1000 genomes]
rs10056038	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10063521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10213754	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10477597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13359038	1.00[EUR][1000 genomes]
rs28662353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28889136	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4620046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57048210	1.00[EUR][1000 genomes]
rs9327133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs951593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023146	chr5:119301891-119623417	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537883	chr5:119301891-119623417	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv432803	chr5:119419101-119659101	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv882782	chr5:119526332-119627087	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv882783	chr5:119532996-119605609	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
7	nsv882784	chr5:119537259-119606988	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv882785	chr5:119557828-119606988	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119589600-119590400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:119590000-119590400	Enhancers	H1 Cell Line	embryonic stem cell
3	chr5:119590000-119590400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:119590000-119590400	Enhancers	HMEC	breast
5	chr5:119590000-119591200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:119590000-119591400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr5:119590000-119591400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr5:119590000-119591600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:119590000-119591800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr5:119590000-119592200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:119590200-119590400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr5:119590200-119591600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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